Visualizing gene set enrichment analysis results (clusterProfiler) using dotHeatmap

import os,sys
import matplotlib.pylab as plt
import pickle
import glob
import numpy as np
import matplotlib as mpl
import pandas as pd
mpl.style.use('default')
mpl.rcParams['pdf.fonttype'] = 42
mpl.rcParams['ps.fonttype'] = 42
mpl.rcParams['font.family'] = 'sans-serif'
mpl.rcParams['font.sans-serif'] = 'Arial'
mpl.rcParams['figure.dpi'] = 80
mpl.rcParams['savefig.dpi']=300
import pickle
sys.path.append(os.path.expanduser("~/Projects/Github/PyComplexHeatmap"))
import PyComplexHeatmap
print(PyComplexHeatmap.__version__)
from PyComplexHeatmap import *

1.7.2.dev0+g8abf70a.d20240415

Why do we need a better way to visualize the gene set enrichment analysis result?

Traditionally, we have to plot lots of barplot or dotplot to visualize the gene set enrichment analysis. For example:

What if we had lots of cell types and performed gene set enrichment analysis for each cell types? It is not a good idea to plot lots of barplot or dotplot in the manuscript.

In this case, we can merge all the enriched result into one matrix and plot a dotHeatmap using PyComplexHeatmap

Read data

In this example dataset, we have 2 groups and 3 different cell types in each group, and we have already gotten the GO Biological Process (BP), Molecular Function (MF) and KEGG Pathway enrichment result using R package clusterProfiler and merged the results into one matrix.

with open("../data/enrichment_analysis_dotHeatmap.pickle",'rb') as f:
    data1,df_row,df_col,colors=pickle.load(f)

data1

	ID	Description	GeneRatio	p.adjust	Count	Group	CellType	EnrichedCategory	-log10(p.adjust)	ColID	RowID
0	GO:0003779	actin binding	0.044949	2.453212e-41	186	Group2	CT1	MF	40.610265	Group2-CT1	MF||actin binding
1	GO:0030695	GTPase regulator activity	0.043016	6.744023e-40	178	Group2	CT1	MF	39.171081	Group2-CT1	MF||GTPase regulator activity
2	GO:0060589	nucleoside-triphosphatase regulator activity	0.043016	6.744023e-40	178	Group2	CT1	MF	39.171081	Group2-CT1	MF||nucleoside-triphosphatase regulator activity
3	GO:0005201	extracellular matrix structural constituent	0.021266	5.810239e-35	88	Group2	CT1	MF	34.235806	Group2-CT1	MF||extracellular matrix structural constituent
4	GO:0050839	cell adhesion molecule binding	0.031899	1.612420e-31	132	Group2	CT1	MF	30.792522	Group2-CT1	MF||cell adhesion molecule binding
...	...	...	...	...	...	...	...	...	...	...	...
840	GO:0050905	neuromuscular process	0.010454	1.224335e-07	122	Group2	CT2	BP	6.912100	Group2-CT2	BP||neuromuscular process
1205	GO:0030534	adult behavior	0.009426	6.028861e-06	110	Group2	CT2	BP	5.219765	Group2-CT2	BP||adult behavior
1558	GO:0035019	somatic stem cell population maintenance	0.004799	6.029991e-05	56	Group2	CT2	BP	4.219683	Group2-CT2	BP||somatic stem cell population maintenance
1746	GO:0019827	stem cell population maintenance	0.009854	1.467128e-04	115	Group2	CT2	BP	3.833532	Group2-CT2	BP||stem cell population maintenance
2999	GO:0021953	central nervous system neuron differentiation	0.008997	9.138960e-03	105	Group2	CT2	BP	2.039103	Group2-CT2	BP||central nervous system neuron differentiation

139 rows × 11 columns

df_row

	EnrichedCategory	Description
RowID
MF||actin binding	MF	actin binding
MF||GTPase regulator activity	MF	GTPase regulator activity
MF||nucleoside-triphosphatase regulator activity	MF	nucleoside-triphosphatase regulator activity
MF||extracellular matrix structural constituent	MF	extracellular matrix structural constituent
MF||cell adhesion molecule binding	MF	cell adhesion molecule binding
MF||metal ion transmembrane transporter activity	MF	metal ion transmembrane transporter activity
MF||monoatomic ion channel activity	MF	monoatomic ion channel activity
MF||monoatomic ion gated channel activity	MF	monoatomic ion gated channel activity
MF||gated channel activity	MF	gated channel activity
MF||calmodulin binding	MF	calmodulin binding
MF||transmembrane receptor protein kinase activity	MF	transmembrane receptor protein kinase activity
BP||cell-substrate adhesion	BP	cell-substrate adhesion
BP||extracellular structure organization	BP	extracellular structure organization
BP||extracellular matrix organization	BP	extracellular matrix organization
BP||external encapsulating structure organization	BP	external encapsulating structure organization
BP||axon guidance	BP	axon guidance
BP||locomotory behavior	BP	locomotory behavior
BP||adult behavior	BP	adult behavior
BP||fat cell differentiation	BP	fat cell differentiation
BP||neuromuscular process	BP	neuromuscular process
BP||central nervous system neuron differentiation	BP	central nervous system neuron differentiation
BP||central nervous system neuron development	BP	central nervous system neuron development
BP||stem cell population maintenance	BP	stem cell population maintenance
BP||somatic stem cell population maintenance	BP	somatic stem cell population maintenance
KEGG||Amphetamine addiction	KEGG	Amphetamine addiction
KEGG||Calcium signaling pathway	KEGG	Calcium signaling pathway
KEGG||Cocaine addiction	KEGG	Cocaine addiction
MF||cytokine activity	MF	cytokine activity
KEGG||Cytokine-cytokine receptor interaction	KEGG	Cytokine-cytokine receptor interaction
KEGG||Neuroactive ligand-receptor interaction	KEGG	Neuroactive ligand-receptor interaction
KEGG||Cytoskeleton in muscle cells	KEGG	Cytoskeleton in muscle cells
KEGG||ECM-receptor interaction	KEGG	ECM-receptor interaction
KEGG||Viral protein interaction with cytokine and cytokine receptor	KEGG	Viral protein interaction with cytokine and cy...
KEGG||Focal adhesion	KEGG	Focal adhesion
KEGG||Axon guidance	KEGG	Axon guidance
KEGG||Systemic lupus erythematosus	KEGG	Systemic lupus erythematosus
KEGG||ATP-dependent chromatin remodeling	KEGG	ATP-dependent chromatin remodeling
MF||methylation-dependent protein binding	MF	methylation-dependent protein binding
MF||methylated histone binding	MF	methylated histone binding
MF||modification-dependent protein binding	MF	modification-dependent protein binding

df_col

	Group	CellType
Group2-CT1	Group2	CT1
Group1-CT2	Group1	CT2
Group1-CT3	Group1	CT3
Group2-CT3	Group2	CT3
Group1-CT4	Group1	CT4
Group1-CT1	Group1	CT1
Group2-CT2	Group2	CT2

Plot

s_min,s_max=data1.GeneRatio.min(),data1.GeneRatio.max()

data1.loc[data1.GeneRatio==s_min]

	ID	Description	GeneRatio	p.adjust	Count	Group	CellType	EnrichedCategory	-log10(p.adjust)	ColID	RowID
3074	GO:0021954	central nervous system neuron development	0.004586	0.027429	42	Group2	CT3	BP	1.561784	Group2-CT3	BP||central nervous system neuron development

data1.loc[data1.GeneRatio==s_max]

	ID	Description	GeneRatio	p.adjust	Count	Group	CellType	EnrichedCategory	-log10(p.adjust)	ColID	RowID
1	GO:0045444	fat cell differentiation	0.176471	0.000382	6	Group1	CT1	BP	3.417494	Group1-CT1	BP||fat cell differentiation

left_ha = HeatmapAnnotation(
                          label=anno_label(df_row.EnrichedCategory, merge=True,rotation=0,colors=colors,relpos=(1,0.8)),
                          Category=anno_simple(df_row.EnrichedCategory,cmap='Set1',
                                           add_text=False,legend=False,colors=colors),
                           axis=0,verbose=0,label_kws={'rotation':45,'horizontalalignment':'left','visible':False})
right_ha = HeatmapAnnotation(
                          label=anno_label(df_row.Description, merge=True,rotation=0,relpos=(0,0.5),arrowprops=dict(visible=True),
                                           colors=df_row.assign(color=df_row.EnrichedCategory.map(colors)).set_index('Description').color.to_dict(),
                                          fontsize=12,luminance=0.8,height=2),
                           axis=0,verbose=0,label_kws={'rotation':45,'horizontalalignment':'left'},
                            orientation='right')

col_ha = HeatmapAnnotation(
                           Group=anno_simple(df_col.Group,cmap='Set1',legend=False,add_text=True,
                                               height=4.5,colors={'Group1':'yellowgreen','Group2':'orange'}),
                           CellClass=anno_simple(df_col.CellType,cmap='Set1',legend=False,add_text=True,
                                                 height=4.5),
                           verbose=0,label_side='right',label_kws={'horizontalalignment':'left'})

plt.figure(figsize=(4, 8))
cm = DotClustermapPlotter(data=data1, x='ColID',y='RowID',value='-log10(p.adjust)',c='-log10(p.adjust)',s='GeneRatio',
                          row_cluster=True,col_cluster=True,hue='Group',
                          cmap={'Group1':'Greens','Group2':'OrRd'},
                          vmin=-1*np.log10(0.1),vmax=-1*np.log10(1e-10),
                          colors={'Group1':'yellowgreen','Group2':'orange'},
                          marker={'Group1':'*','Group2':'$\\ast$'},
                          show_rownames=True,show_colnames=False,row_dendrogram=False,
                          col_names_side='top',#row_names_side='right',
                          xticklabels_kws={'labelrotation': 30, 'labelcolor': 'blue','labelsize':14},
                          top_annotation=col_ha,left_annotation=left_ha,right_annotation=right_ha,
                          spines=False,
                          row_split=df_row.EnrichedCategory, row_split_gap=1,
                          col_split=df_col.Group,col_split_gap=0.5,
                          verbose=1,legend_gap=8,
                          #dot_legend_marker='*',
                          # xlabel=Group,xlabel_side="top",
                          # xlabel_kws=dict(labelpad=8,fontweight='bold'),
                          # xlabel_bbox_kws=dict(facecolor=facecolor)
                         )
# cm.ax_heatmap.grid(which='minor',color='black',linestyle='--',linewidth=1)
for ax in cm.heatmap_axes.ravel():
    ax.grid(axis='both',which='major',color='black',linestyle='dashdot',alpha=0.1)
    # for side in ["top", "left", "bottom"]:
    #     ax.spines[side].set_visible(True)
    #     ax.spines[side].set_color('grey')
    #     ax.spines[side].set_linewidth(1)
    #     ax.spines[side].set_linestyle('--')
# plt.savefig(f"cell_class_dotHeatmap.pdf",bbox_inches='tight')
plt.show()

Starting plotting..
Starting calculating row orders..
Reordering rows..
Starting calculating col orders..
Reordering cols..
Plotting matrix..
Inferred max_s (max size of scatter point) is: 106.46754159267321
Collecting legends..
Plotting legends..
Estimated legend width: 23.6375 mm

In this example, we used two different kinds of markers and cmap to indicate Group1 and Group2, rows are split by category of enriched terms, sizes of dot/marker indicates gene ratio (The ratio of genes annotated by the GO term in your list to the total number of genes in your list).

How to select marker: